University of SharjahFaculty of health Sciences

Department of Medical Laboratory Sciences

Biology 1Chapter2 ||| Lecture 1

Chapter 2Chemistry of life

• Please note:- Notes to follow are organized according to chap. 2 in the 10th ed. of the

textbook.- These brief notes are meant to help you read and understand the text

material and not to substitute for it.• Learning objectives:• Fundamentals of the chemistry of life: atoms, molecules, compounds,

chemical reactions and chemical bonds.• Inorganic compounds: water, salts, acids, bases, the pH scale …• Organic compounds: polymerization reactions, the chemistry of

macromolecules (sugars, lipids, nucleic acids, proteins).• General intro to the functions of macromolecules in living matter

The hierarchy of life• At the most basic level, life is made of

atoms molecules macromolecules organelles cells may be unicellular (e.g. bacteria)

or multicellular (plants, animals, etc.)

• Multicellular life has higher levels of organization above cells

• For humans cells make up tissues organs organ systems organisms (full human)

• Therefore, one can say that life is Matter

• Matter:

• - It is what we and everything else in the universe is made of.

• - Technically = anything that occupies space and has mass.

• States of matter:

• Solid: has specific volume and shape

• Liquid: has a defined volume but conforms to the shape of the container it occupies

• Gas: No definite volume or shape

• Matter is also energy, so what is energy?

• Energy: ability to do work, 2 types:

• Potential: stored energy like that in chemical bonds, water in tank above the roof, and so on

• Kinetic: energy of motion or energy displayed while the work is being done

• Forms: mechanical, chemical, heat/radiation, electrical, ...etc. It is possible to convert energy from one form to another.

• Example: we eat plants which photosynthesize, so:

• Sun (radiation) absorbed by plants chemical energy (glucose) produced by plants used to produce chemical (food) energy in animals in animal cells it gets converted into chemical energy (proteins and lipids, ATP and so on) mechanical (movement of muscles), heat (metabolism-related body heat), electrical (nerve impulses), etc.

Atoms & elements• An element is a unique substance that cannot be broken down into

simpler substances by conventional approaches• 112 elements are present in nature; 92 occur naturally and 20 are

produced artificially.• C, H, O, & N = 96% of body weight; • The remaining 4% is made up of trace elements ( table 2-1) –Calcium (Ca) bone formation –Phosphorus (P) DNA synthesis –Potassium (K) cell signaling, nervous system –Sulfur (S) –Sodium (Na) –Chlorine (Na) –Magnesium (Mg)

Trace elements are present in trace, or minute quantities, but are extremely important

What about the remaining 0.01%?

–Iron (Fe) – hemoglobin, binds oxygen–Copper (Cu) – enzymes, electron transport–Fluorine (F) – prevents tooth decay, added to municipal water–Iodine (I) – thyroid enzymes (deficiency -> goiter); “iodized salt”

- Each element is made up of small building blocks = atoms

- Atom from Greek for incapable of being divided

- Atoms are made up of small subatomic particles; main ones are protons, neutrons and electrons

- Subatomic particles differ in their mass, electrical charge and location within/around atoms table 2-2

Main Subatomic particles

• Models of atomic structure = orbital vs. planetary

• Planetary = protons + neutrons clustered in the core with electrons orbiting around in designated shells something like a solar system

• Orbital = a dense core of protons + neutrons with electrons represented as a dense cloud of negative charge instead of fixed orbits

Identifying elements• Atomic number: equivalent to number of protons

inside the atom (= number of electrons) >> why? • Atomic mass: Σ protons + neutrons [but not electron

as weight of electrons (1/800 that of protons) is negligible]

• Atomic weight: same as atomic mass for atoms with non-variable atomic structure . For certain elements, the number of neutrons (but not protons or electrons) in the atom vary = isotopes. Hence the mass of the atom changes = atomic weight is used to denote a changing atomic mass of the element

Isotopes• All isotopes of an element have the same atomic number

but different atomic mass• All isotopes exhibit the same chemical properties (fixed

number of electrons)• Atomic weight of an element = atomic mass of the most

abundant isotope of the element• Example: Hydrogen has an atomic number of 1 but it has 3

isotopes with atomic masses 1, 2 or 3. Atomic weight of H = 1.0079 which is ~ atomic mass of 1H (the most abundant isotope of H).

• Heavier isotopes of an atom are less stable than lighter ones decay or decompose fast so as to stabilize radioisotopes

•Radioisotopes are radioactive = emit (generate) electromagnetic particles ( or = energy •Particles can be detected, hence use of isotopes as biological tracers in research (125I, 32P, 35S, 3H) or in medical diagnostic imaging (PET scanning, iodine uptake activity of the thyroid gland, etc.).

•Some particles have high energy to destroy /change the structure of certain molecules like DNA hence their use in radiotherapy radioactive cobalt or radium in cancer therapy.

**For more on the medical use of radioisotopes see pages 10-11 in textbook

Molecules and Compounds: • When 2 or more atoms of the same element

combine = molecules form O2 and H2 are molecules• When 2 or more atoms of different elements

combine = compounds form NaCl, H2O, CH4 are compounds

• In practice, the two terms are interchangeable?• When a compound forms it acquires a number of

emergent properties that differ from those of the forming atoms (boiling point, freezing point, chemical behavior, etc).

• Chemical bonds and chemical reactions

• - Electrons are distributed around the dense core of atoms in shells (orbitals); 1st shell takes only 2 electrons to fill up (stabilize) that is why atoms of helium He2 are stable (nonreactive or inert), shells 2, 3, …. 7 each takes 8 electrons to be complete.

- Number of electrons in the last shell (valence shell) is key in determining the chemical bonding behavior of atoms

- If valence shell of an atom has 2 (helium) or 8 (Neon, Argon, Xenon, …etc) electrons = stable atom non-reactive = inert substance

Reactive vs. nonreactive (inert) elements

Chemical Bonding

Ionic bonds: total transfer of an electron from one atom into another atom atoms that loses the electron become positively charged (cation) and that which acquires the electron becomes negatively charged (anion)

Covalent bonds:• Form between similar or different atoms with valence shells

lacking more than one electron or requiring more than one electron to complete their valence shells (except for hydrogen).

• Sharing of a pair of electrons between 2 atoms• Examples: C and C, C and H, O and O, O and H, N and H, etc.• A covalent bond could be non-polar = both atoms have the

same affinity for electrons or polar = one atom has high affinity for electrons than the other atom

• Covalent bonds that form between 2 identical atoms is always non-polar; example C-C

• C-H is also non-polar as the affinity of both C and H for electrons is the same

Hydrogen bonds: forms between atoms in molecules with polar covalent bonds

Example: the covalent bond between oxygen and hydrogen is polar because oxygen loves electrons far more than hydrogen the pair of electrons between the 2 atoms move more towards oxygen more negative charge closer to oxygen and more positive charge closer to hydrogen partially positive hydrogens in water attracts partially negative oxygens present on a different water molecule and vice versa

The hierarchy of life• At the most basic level, life is made of

atoms molecules macromolecules organelles cells may be unicellular (e.g. bacteria)

or multicellular (plants, animals, etc.)

• Multicellular life has higher levels of organization above cells

• For humans cells make up tissues organs organ systems organisms (full human)

Chemical reactions

Absorb energy Release energy Absorb & release energyAnabolic Catabolic Anabolic / catabolic (condensation) (hydrolysis)

Factors that influence the rate of chemical reactions (table 2-4)

• Temperature• Concentration of reactants• Particle size• Catalysts (e.g. enzymes)